GEO series

Enhancer rewiring orchestrates inflammation and loss of cell identity during muscle stem cell aging [RNA-seq]

GSE293130 Mus musculus (mouse) RNA-seq (gene expression) 23 samples Submitted 2025/11/13 Platform GPL21626

At a glance

RNA-seq (gene expression) · mouse · 23 samples

What it is: RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism: Mus musculus (mouse)
Samples: 23 samples: 23 samples, each with a distinct title — no replicated groupsGroups are read from the sample names, not from the paper. Check the list below.
Data you can get: A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Paper: Enhancer Rewiring Orchestrates Inflammation and Loss of Cell Identity During Muscle Stem Cell AgingAging cell · 2026

Summary (written by the submitters)

Loss of regeneration is a key feature of aging organs, often linked to stem cell exhaustion. Skeletal muscle stem cells (MuSCs) undergo age-related numerical and functional decline, contributing to reduced regenerative potential. Using low-input multi-omics, we systematically profiled the epigenome, transcriptome, and 3D genome of MuSCs from individual mice across 3 age groups (young, old, and geriatric) and both sexes.

Read the full summary ↓

At baseline, young male MuSCs showed reduced expression of cell cycle-related mRNAs. In aged mice, particularly males, MuSCs exhibited early alterations (emerging during the transition from young to old age), including enhanced proinflammatory signaling, and loss of cell identity. Late alterations (emerging during the transition from old to geriatric age) included heightened inflammation, widespread enhancer activation, and extensive 3D genome rewiring. Proinflammatory pathways were enriched for interferon signaling and correlated with endogenous retroviral expression and NFκB activity. Late-stage epigenome and 3D genome rewiring reflected downstream degenerative changes in muscle organization, response to cytokines, and loss of myogenic identity. Thus, progressive molecular shifts may explain the aggravated proliferative deficit and functional impairment observed in MuSCs during aging.

Published in

Enhancer Rewiring Orchestrates Inflammation and Loss of Cell Identity During Muscle Stem Cell Aging

Shi C, Yang N, Pizano E et al. · Aging cell 2026 · PMID 41239549 · doi:10.1111/acel.70289

This dataset

Open GSE293130 in finder → Find more mouse RNA-seq datasets →

Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE293130_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1242860 and SRA study SRP573726. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41239549) ↗

Study design

23 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 23 sample titles: 23 distinct titles with little repetition. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study

GSM8877111 YM1_RNA
GSM8877112 YM2_RNA
GSM8877113 YM3_RNA
GSM8877114 YM4_RNA
GSM8877115 YF1_RNA
GSM8877116 YF2_RNA
GSM8877117 YF3_RNA
GSM8877118 OM1_RNA
GSM8877119 OM2_RNA
GSM8877120 OM3_RNA
GSM8877121 OM4_RNA
GSM8877122 OF1_RNA
GSM8877123 OF2_RNA
GSM8877124 OF3_RNA
GSM8877125 OF4_RNA
GSM8877126 GM1_RNA
GSM8877127 GM2_RNA
GSM8877128 GM3_RNA
GSM8877129 GM4_RNA
GSM8877130 GF1_RNA
GSM8877131 GF2_RNA
GSM8877132 GF3_RNA
GSM8877133 GF4_RNA

Datasets on a similar topic

GSE293139 Enhancer rewiring orchestrates inflammation and loss of cell identity during muscle stem cell aging 90 samples shares orchestrates, enhancer, rewiring, identity, muscle, aging, loss
GSE293129 Enhancer rewiring orchestrates inflammation and loss of cell identity during muscle stem cell aging [CUT&RUN] 36 samples shares orchestrates, enhancer, rewiring, identity, muscle, aging, loss
GSE282096 Diminished transcriptional activity and splicing changes drive gene length-biased rewiring in the aging transcriptome (RNA-Seq) 94 samples shares rewiring, rna-seq, aging
GSE294336 BMAL1 and YAP cooperate to hijack enhancers and promote inflammation in the aged epidermis [RNA-seq Aged_adult] 48 samples shares enhancer, rna-seq
GSE267936 Functional Optic Tract Rewiring via Subtype- and Target-specific Axonal Regeneration and Presynaptic Activity Enhancement (bulk RNA-Seq) 40 samples shares rewiring, rna-seq
GSE255061 Phosphatase-independent activity of smooth-muscle calcineurin orchestrates a gene expression program leading to arterial hypertension 40 samples shares orchestrates, muscle
GSE335970 KMT2C catalytic activity regulates enhancer H3K4me1 and synaptic gene expression in cortical excitatory neurons [RNA-Seq] 39 samples shares enhancer, rna-seq
GSE317231 Bcl11a orchestrates multilineage integrity in aging hematopoiesis by regulating multipotent progenitor fate decisions 30 samples shares orchestrates, aging

Search all mouse RNA-seq datasets in GEO →

Share this dataset

Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.